Publication:

Metastasis-resident bacteria in advanced hormone receptor-positive breast cancer are related to primary tumormicrobiota and show distinct composition

Background:Tumor-resident bacteria are an emerging component of the tumormicroenvironment. Recent studies have shown their presence over multiple cancertypes. Lately, mechanistic evidence in a murine breast cancer model indicates thatthese bacteria promote the metastatic process. However, the presence and confor-mation of the microbiome of human metastatic tumors have not been determined.Here, we characterized tumor-resident bacteria in a cohort of metastatic hormonereceptor-positive breast cancer (MHRBC) patients with matched primary tumors. Methods:We performed bacterial 16S rDNA sequencing targeting hypervariable re-gions V2-4 and V6-9 on FFPE tissues from 40 patients with MHRBC and their matchedprimary tumors. Sequence data were processed using high resolution sample infer-ence with DADA2. Controls included normal breast tissue, paraffin from all blocks anda simulated bacterial community, comprising known intra and extracellular bacteria.Taxonomy was assigned using the SILVA database v138. Feature selection was used todetermine amplicon sequences in primary tumors related to their metastasis. Amachine learning classifier was generated to predict the metastatic site from selectedamplicons. Results:a-diversity was similar among sample types, whileb-diversity showedsegregation between metastatic and primary tumors.Alphaproteobacteria,Gam-maproteobacteriaandBacillihad increased relative abundance across metastatic andprimary tumors. Differential abundance ofProteobacteriaandFirmicutesspecies wasidentified in metastatic tumors. A machine learning classifier using the 5 top rankedamplicons in primary tumors was capable of 100% precision and high recall forprediction of bone and liver metastatic site, but not lung metastases. Conclusions:We identified and categorized the tumor-resident bacteria of MHRBC. Toour knowledge, this is thefirst study looking at the composition of metastatic breastcancer microbiome. While insights have been gained on primary tumor microbiota,the role of metastasis-resident bacteria including local immunity and treatmentresistance warrants further study